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Recent Releases of cobra

cobra - 0.29.1

Release notes for cobrapy 0.29.1

New features

Fixes

  • Fixes the incorrect bounds in the CycleFree loop removal.
  • Fixes reduced costs and shadow prices not available when using non-convex models.
  • Fixed a bug with SBML group parsing that affects the Debian package.
  • Fixed a bug where loadmatlabmodel would not work with numpy 2.0.

Other

  • Adding a duplicate boundary reaction (with add_boundary) no longer errors, but instead just returns the existing reaction.
  • Automatic detection of the external compartment now recognizes CARVEME and GAPSEQ ids and will no longer show a warning for models generated with those tools.

Deprecated features

Backwards incompatible changes

- Python
Published by github-actions[bot] over 1 year ago

cobra - 0.29.0

Release notes for cobrapy 0.29.0

New features

  • Added a new "hybrid" solver that exposes an HIGHS/OSQP combinations for large scale LPs, MILPs, and QPs.

Fixes

Repaired the broken Biomodels Web IO.

Other

Deprecated features

  • The OSQP solver is deprecated in favor of the hybrid solver which also uses OSQP but will not attempt to solve LPs with OSQP anymore. Setting the model.solver = "osqp" will now use the hybrid interface and will raise an error in a future release.

Backwards incompatible changes

- Python
Published by github-actions[bot] over 2 years ago

cobra - 0.28.0

Release notes for cobrapy 0.28.0

Fixes

  • Allowed for pandas versions >=1.0 and <3.0 (#1364).

Other

  • Updated the GitHub Actions used (#1364).

Backwards incompatible changes

  • Updated the package depinfo to version >2 (#1361).

- Python
Published by github-actions[bot] over 2 years ago

cobra - 0.27.0

Release notes for cobrapy 0.27.0

New features

Fixes

COBRApy is now compatible with pydantic version 2.

COBRApy is now compatible with the latest numpy versions and pin to a lower version has been removed.

loopless_solution now fixes the objective to its optimum as in the originally published method and returns the objective value in the solution object.

Repair a broken test for fix_objective_as_constraint.

Other

Backwards compatibility for pickled models has been improved.

Deprecated features

Backwards incompatible changes

- Python
Published by github-actions[bot] over 2 years ago

cobra - 0.26.3

Release notes for cobrapy 0.26.3

New features

Fixes

Fixed an issue where reaction bounds were being overwritten by global model min/max values when writing sbml model to file. See #1300.

Fix an issue where runfrog does not work via github actions or local installation by removing the use of obsolete numpy aliases for float and bool.

Fix a bug where installing httpx>=0.24 would break cobrapy IO.

Other

Deprecated features

Backwards incompatible changes

- Python
Published by github-actions[bot] about 3 years ago

cobra - 0.26.2

Release notes for cobrapy 0.26.2

New features

Fixes

Fix the version numbers, my bad - cd

Other

Deprecated features

Backwards incompatible changes

- Python
Published by github-actions[bot] over 3 years ago

cobra - 0.26.1

Release notes for cobrapy 0.26.1

New features

Fixes

Fix automatic building of the documentation.

Fix an issue where SBML models with a "created" date would break lots of the cobrapy functionality.

Temporary fix of restricting numpy to <1.24 as that release introduces breaking changes both in cobrapy and dependencies

Other

Deprecated features

Backwards incompatible changes

- Python
Published by github-actions[bot] over 3 years ago

cobra - 0.26.0

Release notes for cobrapy 0.26.0

New features

  • View number of genes in model notebook representation.
  • added support for Python 3.11

Fixes

  • serializes GPRs to strings to avoid massive storage usage
  • Reformatted example files (ecolicore.xml, mini_cobra.xml, mini.json, mini.yml, textbook.xml.gz) to be more compliant with identifiers.org.
  • ncbigi is not a valid identifiers.org, so it was replaced with ncbiprotein.
  • make sbml.py subsystem reading add partonomy, which matches the definition of SBO:0000633 (see https://sourceforge.net/p/sbo/term-request/113/)
  • Correct reading and writing of subsystem in mat.
  • General cleanup of code in mat.py
  • fix the pandas deprecation warning in find_external_compartment
  • fix an issue where creating a Formula object would give a recursion error

Other

  • Resolve flake8 issues and add missing type annotations and docstrings in src/cobra/io and tests/test_io (#1212).
  • Updated model.py and test_model.py to Python 3.6+, including type annotations and docstrings.
  • Resolve remaining flake8 issues and enable the check in GitHub Actions Lint workflow (#1272).

Deprecated features

  • dropped support for Python 3.6

Backwards incompatible changes

  • Removed model.add_reaction() and replaced remaining usages of it with model.add_reactions()
  • Removed the following tests: testaddremovereactionbenchmark, testaddreaction, testaddreactioncontext, testaddreactionfromothermodel, testaddcobra_reaction
  • Removed model.__add__ and model.__iadd__ - use model.merge to replace them.
  • Remove Model().description().
  • Remove Model().get_metabolite_compartments().

- Python
Published by github-actions[bot] over 3 years ago

cobra - 0.25.0

Release notes for cobrapy 0.25.0

New features

  • Add knock_out_model_genes to simulate knock-outs, setting reaction bounds of affected reactions to zero and returning a list of reactions that were knocked-out. Replaces delete_model_genes and undelete_model_genes since it is context sensitive.
  • Improve reading of matlab models which will include metabolite and reaction annotations.

Fixes

  • model.copy() will now correctly copy GPRs.
  • Fix an error where matlab models can not be read if their bounds exceed the configuration default in some cases.
  • Fixed some bugs in GPR().from_string() where it was using the unmodified string, leading to errors with GPRs that should work. Made GPRs that have empty parenthesis fail more comprehensibly.

Other

  • Move tests to a different directory, from src/cobra/test to tests (#1191).
  • Add two tests for GPR fixes:
    • test_gpr_wrong_input()
    • test_gpr_that_needs_two_replacements()
  • Clean up Python syntax (#1152, #1153, #1171, #1173, #1182)

Deprecated features

  • Deprecate delete_model_genes, undelete_model_genes

Backwards incompatible changes

  • Remove find_gene_knockout_reactions from delete.py
  • Remove _find_gene_knockout_reactions_fast, _gene_knockout_computation, _get_removed from test_delete.py
  • Remove pymatlib direct transfer of models to matlab process. Please use save_matlab_model() and then read the model in matlab.

- Python
Published by github-actions[bot] about 4 years ago

cobra -

Release notes for cobrapy 0.24.0

New features

  • Gene-protein-reaction association rules are now represented by a structured object GPR. Reaction.gene_reaction_rule still returns a string and a string can be assigned to it that will modify the underlying GPR instance.
  • The Reaction class has gained another attribute Reaction.gpr which allows direct access to the GPR instance (#1143).

Fixes

  • Syntax update and type annotations (#1151).

- Python
Published by Midnighter about 4 years ago

cobra - 0.23.0

Release notes for cobrapy 0.23.0

Fixes

  • Make compatible with Python 3.10
  • Use the internal semantic GPR parser in the SBML module
  • Setting a growth medium will not reset export flux bounds anymore

Other

  • Clean up code (#1116, #1114, #1113, #1111, #1110, #1097)

- Python
Published by github-actions[bot] over 4 years ago

cobra - 0.22.1

Release notes for cobrapy 0.22.1

Fixes

  • Fix an old bug with double gene deletion that was not knocking-out combinations (#1103).
  • Lots of syntax, annotation, and docstring fixes (#1081, #1083, #1084, #1085, #1086, #1088, #1090, #1091, #1092, #1093, #1094, #1095, #1096).

Deprecated features

  • find_gene_knockout_reactions is deprecated.

- Python
Published by github-actions[bot] almost 5 years ago

cobra - 0.22.0

Release notes for cobrapy 0.22.0

New features

  • Add support for the OSQP and COIN-OR CBC solvers (#946)

Fixes

  • Fix the Reaction.compartments attribute not updating after metabolite changes (#1055)
  • Lots of syntax, annotation, and docstring fixes (#1058, #1059, #1060, #1063, #1065, #1066, #1076, #1077, #1080)
  • Multiprocessing on windows now sends data to processes via a pickle file which should speed up any multiprocessing initialization (#1070)
  • Upgrade optlang and fix some tolerance issues (#1011)
  • Enable Python 3.9 (#1082)

Documentation

  • Document boundary reactions (#1038)
  • Documentation is now built again on each release (#1047)
  • Clarify pfba in the documentation (#1049)

Other

  • COBRApy source code releases are now deposited on Zenodo which provides a citeable DOI (#1061)
  • COBRApy creates automatic releases to BioSimulators (#1064)
  • Fix deployment of releases to the website (#1068)
  • Improve the pyproject.toml config (#1067)

Backwards incompatible changes

  • Remove some particular cobra.Reaction.lower_bound and .upper_bound behaviour that has been deprecated for a long time.

- Python
Published by github-actions[bot] about 5 years ago

cobra - Test Dispatch ref fix

- Python
Published by Midnighter about 5 years ago

cobra - Test BioSimulators Dispatch

- Python
Published by Midnighter about 5 years ago

cobra - Test Zenodo integration

- Python
Published by Midnighter about 5 years ago

cobra - 0.21.0

Release notes for cobrapy 0.21.0

Other

  • Update libSBML dependency to python-libsbml==5.19.0.
  • Docstring and style changes.

- Python
Published by github-actions[bot] over 5 years ago

cobra - 0.20.0

Release notes for cobrapy 0.20.0

New features

  • There is a new function inspired by cameo that can load models directly from BiGG or BioModels and by default will cache them locally (#995), for example,

    ```py from cobra.io import load_model

    ecoli = loadmodel("iML1515") ylipo = loadmodel("MODEL1604280017") ```

Fixes

  • Over a series of pull requests, @synchon has been modernizing parts of the codebase for Python 3.6+ (#993, #999, #1000, #1003)
  • Upgrade the dependency python-libsbml-experimental to 5.18.3

- Python
Published by github-actions[bot] over 5 years ago

cobra - 0.18.1

Release notes for cobrapy 0.18.1

Fixes

  • Use the correct SBO term for unbounded (infinite bounds) reactions.

Other

  • Pin dependency on python-libsbml-experimental 5.18.1.

- Python
Published by Midnighter almost 6 years ago

cobra - 0.18.0

Release notes for cobrapy 0.18.0

New features

  • Support writing SBML notes on model objects

Fixes

  • Test alternative solver
  • Handle repeated infeasible optimizations in minimal_medium
  • Allow newline characters in SBML notes

Backwards incompatible changes

  • Change the container type of groups from set to DictList
  • Expect annotation attributes to be of type dict

Internal

  • Update Travis CI configuration
  • Add Python 3.8 to PyPI classifiers

Contributors

  • @BenjaSanchez
  • @cdiener
  • @ecederstrand
  • @Hemant27031999

- Python
Published by Midnighter almost 6 years ago

cobra - 0.19.0

Release notes for cobrapy 0.19.0

We now have an official code of conduct and a committee of three people to handle reports! You can contact them at conduct@opencobra.org. You can also contact them individually at:

Many thanks to them for taking on this responsibility.

New features

  • Deletion result DataFrames as returned by functions from cobra.deletions now have a new knockout accessor. See the docs on usage examples.
  • All summaries are now persistent objects. The same summary can be displayed in multiple ways. The underlying data for the summary can also be accessed.
  • The model summary now displays elementary (by default carbon) uptake and secretion.
  • The JSON schema is now available as a stand-alone JSON file.

Fixes

  • Remove the frozenset indexing in deletion DataFrames that is now unsupported in pandas.
  • Summaries for models, metabolites, and reactions are now calculated instantaneously and thus also work with model contexts.
  • JSON models can now contain infinity and NaN values as bounds.
  • The Matlab bridge for reading Matlab models should be restored. Any testing or problem reports are greatly appreciated.

Deprecated features

  • We are progressively updating our codebase. That means that more and more parts will require Python 3.6+.

Backwards incompatible changes

  • Deletion result DataFrames have no frozenset index anymore but now carry the deleted elements in the ids column.

- Python
Published by Midnighter almost 6 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.17.1

Please see https://github.com/opencobra/cobrapy/tree/0.17.1/release-notes/0.17.1.md for the full release notes.

- Python
Published by cobrapy-bot over 6 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.17.0

Please see https://github.com/opencobra/cobrapy/tree/0.17.0/release-notes/0.17.0.md for the full release notes.

- Python
Published by cobrapy-bot over 6 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.16.0

Please see https://github.com/opencobra/cobrapy/tree/0.16.0/release-notes/0.16.0.md for the full release notes.

- Python
Published by cobrapy-bot almost 7 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.15.4

Please see https://github.com/opencobra/cobrapy/tree/0.15.4/release-notes/0.15.4.md for the full release notes.

- Python
Published by cobrapy-bot almost 7 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.15.3

Please see https://github.com/opencobra/cobrapy/tree/0.15.3/release-notes/0.15.3.md for the full release notes.

- Python
Published by cobrapy-bot about 7 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.15.2

Please see https://github.com/opencobra/cobrapy/tree/0.15.2/release-notes/0.15.2.md for the full release notes.

- Python
Published by cobrapy-bot about 7 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.15.1

Please see https://github.com/opencobra/cobrapy/tree/0.15.1/release-notes/0.15.1.md for the full release notes.

- Python
Published by cobrapy-bot about 7 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.14.2

Please see https://github.com/opencobra/cobrapy/tree/0.14.2/release-notes/0.14.2.md for the full release notes.

- Python
Published by cobrapy-bot over 7 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.14.1

Please see https://github.com/opencobra/cobrapy/tree/0.14.1/release-notes/0.14.1.md for the full release notes.

- Python
Published by cobrapy-bot over 7 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.14.0

Please see https://github.com/opencobra/cobrapy/tree/0.14.0/release-notes/0.14.0.md for the full release notes.

- Python
Published by cobrapy-bot over 7 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.13.4

Please see https://github.com/opencobra/cobrapy/tree/0.13.4/release-notes/0.13.4.md for the full release notes.

- Python
Published by cobrapy-bot almost 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.13.3

Please see https://github.com/opencobra/cobrapy/tree/0.13.3/release-notes/0.13.3.md for the full release notes.

- Python
Published by cobrapy-bot almost 8 years ago

cobra - 0.13.1

Failed PyPI deployment due to mismatching email addresses.

- Python
Published by Midnighter almost 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.13.0

Please see https://github.com/opencobra/cobrapy/tree/0.13.0/release-notes/0.13.0.md for the full release notes.

- Python
Published by cobrapy-bot almost 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.12.1

Please see https://github.com/opencobra/cobrapy/tree/0.12.1/release-notes/0.12.1.md for the full release notes.

- Python
Published by cobrapy-bot almost 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.12.0

Please see https://github.com/opencobra/cobrapy/tree/0.12.0/release-notes/0.12.0.md for the full release notes.

- Python
Published by cobrapy-bot about 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.11.3

Please see https://github.com/opencobra/cobrapy/tree/0.11.3/release-notes/0.11.3.md for the full release notes.

- Python
Published by cobrapy-bot about 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.11.2

Please see https://github.com/opencobra/cobrapy/tree/0.11.2/release-notes/0.11.2.md for the full release notes.

- Python
Published by cobrapy-bot over 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.11.1

Please see https://github.com/opencobra/cobrapy/tree/0.11.1/release-notes/0.11.1.md for the full release notes.

- Python
Published by cobrapy-bot over 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.11.0

Please see https://github.com/opencobra/cobrapy/tree/0.11.0/release-notes/0.11.0.md for the full release notes.

- Python
Published by cobrapy-bot over 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.10.1

Please see https://github.com/opencobra/cobrapy/tree/0.10.1/release-notes/0.10.1.md for the full release notes.

- Python
Published by cobrapy-bot over 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.10.0

Please see https://github.com/opencobra/cobrapy/tree/0.10.0/release-notes/0.10.0.md for the full release notes.

- Python
Published by cobrapy-bot over 8 years ago

cobra - https://github.com/opencobra/cobrapy/releases/tag/0.9.1

Please see https://github.com/opencobra/cobrapy/tree/0.9.1/release-notes/0.9.1.md for the full release notes.

- Python
Published by cobrapy-bot over 8 years ago

cobra - 0.9.0

Release notes for cobrapy 0.9.0

Fixes

  • Model.compartment is now a dynamic property fetching the compartments from all metabolites therefore always up-to-date. Assigning a dictionary to the same property updates the internal dictionary of compartment descriptions. This change removes the need for the check for missing compartments from validation.check_metabolite_compartment_formula.
  • Excessively long output of html representations in jupyter notebooks are now abbreviated #577.
  • Reaction forward and reverse variables are no longer cached with those object. No visible effect but simplifies the code.
  • Fix bug in summary methods when used with exchange reaction sas objective. #595.

New features

  • Model.objective_direction is a new revertible property to set maximization / minimization using the context manager.
  • Change output of production_envelope to wide data frame format #587. Also allow multiple carbon source reactions and better handling of zero-division exceptions.
  • Enable summing lists of reactions, see #596

Deprecated features

  • Model.get_metabolite_compartments is deprecated (use Model.compartments instead).
  • Reaction.get_compartments is deprecated (use Reaction.compartments instead).

Backwards incompatible changes

  • The format of the dataframe production_envelope changed listing max and min on different columns instead of the same.

- Python
Published by Midnighter over 8 years ago

cobra - 0.8.2

Release notes for cobrapy 0.8.2

Fixes

  • Guarantee that sampler._reproject always returns a feasible point and will not attempt to reproject already feasible points. #564
  • Model.summary no longer fails when calling after the model has changed. Fixed by letting the summary function re-compute a solution (default) or letting user supply a prior computed solution object. #566
  • Metabolites must now have valid identifiers before being added to a model or ValueError is raised.
  • Fix use of underscores in key/value pairs in legacy sbml notes. #547

Backwards incompatible changes

  • the Solution class no longer contains links progenitor model's reactions and metabolites. Removed since it those can change after the solution has been computed making them erroneous. This of course implies that Solution constructor changes to: def __init__(self, objective_value, status, fluxes, reduced_costs=None, shadow_prices=None, **kwargs):

- Python
Published by hredestig almost 9 years ago

cobra - 0.8.1

Release notes for cobrapy 0.8.1

Fixes

  • Fix bug related to inhomogeneous sampling #558. During flux sampling, store the nullspace rather than the entire projection (N * N.T) which reduces the memory footprint since it uses memory in the order of 2 * n_reaction * n_metabolites instead of 4 * n_reactions^2 (no change in speed). PR #556

- Python
Published by hredestig almost 9 years ago

cobra - 0.8.0

Release notes for cobrapy 0.8.0

Fixes

  • Tests no longer generates warnings about using deprecated functions.
  • Gapfilling integrality thresholds now supported for all optlang solvers.

New features

  • Model.slim_optimize() can be used perform optimization without creating a solution. Can lead to significant speedup compared to Model.optimize when repeatedly doing optimizations and only making use of the objective value as avoiding the need to fetch all values from the solver object.
  • solution, model, metabolite and reaction now have html representation so they give more informative prints in jupyter notebooks.
  • New convenience functions cobra.flux_analysis.find_essential_genes and cobra.flux_analysis.find_essential_reactions.
  • Model.optimize has new parameter raise_error to enable option to get trigger exception if no feasible solution could be found.
  • str(reaction) now gives the more useful reaction id and the reaction string.

Deprecated features

  • str(reaction) no longer gives reaction.id.

- Python
Published by hredestig almost 9 years ago

cobra - 0.7.0

Release notes for cobrapy 0.7.0

Fixes

  • cobra.flux_analysis.reaction.assess was broken following the release of 0.6.0 and has now been fixed (and now with unit tests).
  • production_envelope failed when model C-source was formulated as -> x instead of x <-. Fixed added option to guess the C-source by taking the medium reaction with the highest input C flux.
  • model_to_pymatbridge needs scipy and that's correctly handled now.

New features

  • flux_variability_analysis now has the pfba_factor parameter which enables the inclusion of a constraint on the max sum of absolute fluxes when doing FVA.

Deprecated features

  • cobra.flux_analysis.reaction.assess_{precursors,products} were essentially copies of each other and have been merged to cobra.flux_analysis.reaction.assess_component

- Python
Published by hredestig almost 9 years ago

cobra - 0.6.2

Release notes for cobrapy 0.6.2

Fixes

  • Fix in the ordering and rounding of FVA summary #525
  • Shared memory, improve speed during sampling #521
  • Debug model.remove_reactions to properly work with context manager. This lead to the deprecation of reaction.delete as this was not compatible with the concept of being able to later revert the change. #506, #508.
  • Adding two models (modela + modelb) again results in a model with the objective set to the sum of the two models objectives #505.
  • When adding reactions to a model, the reactions with identifiers identical to those in the model are ignored. #511

New features

  • model.merge can be used to merge two models, more flexibly than the overloaded + and += operators.

Deprecated features

  • reaction.delete has been deprecated in favor of reaction.remove_from_model
  • overloaded + and += for cobra.Model are deprecated in favor of model.merge

- Python
Published by hredestig almost 9 years ago

cobra - 0.6.1

Release notes for cobrapy 0.6.1

Fixes

  • Debug metabolite.add_metabolites with combine=False #503
  • Fix broken printing of metabolites (#502), by removing unnecessary Frozendict

- Python
Published by hredestig about 9 years ago

cobra - 0.6.0

Highlights

In this release we have made major changes to pretty much all corners of cobrapy and we hope that you will enjoy the new features as much as we do, and that any negative impacts on existing workflows will be limited.

The major change is the ongoing move away from cobrapy's internal solver interfaces to those provided by optlang which provides a single unified interface to glpk, cplex and gurobi enhanced by the ability to deal with symbolic expressions. This means formulating complex constraints no longer implies defining the necessary matrix algebra, but instead simply writing the expression and assigning that as an objective to the model.

We feel that this, and the clarified scope and focus attained by separating the topic of linear programming (optlang) and metabolic flux analysis (cobrapy) to two packages is natural and makes both of these tasks less confusing and more fun. We hope that you after trying, feel the same and that in any case you let us know what you think by raising an issue or talking directly to us on gitter or google groups.

New features

The optlang solver interface

The main change is the addition of model.solver which is the optlang interface to the chosen solver (cplex and glpk are currently well supported, gurobi interface is at the time of writing mostly working but improvements are still expected). The solver interface manages variables, constraints and the objective of the model and the task of turning these into a model formulation to be optimized by the solver. From cobrapy's point-of-view, this means that all aspects concerning generating problems, configuring solvers are handed over to optlang and consequently the whole cobra.solver has been deprecated, slated for removal in the next major release of cobrapy.

Importantly, configuring the solver by passing **solver_args or solver='solver' is now instead done by assigning solver to model.solver and then configuring via model.solver.configuration.

Creating new algorithms has been greatly facilitated as it no longer requires formulating objectives and constraints by matrix algebra but instead directly by expressions, e.g. see the implementation of cobra.flux_analysis.moma.add_moma and cobra.flux_analysis.loopless.loopless_solution.

Instead of having only reactions as variables and metabolites as constraints, with optlang, cobrapy now supports arbitrary constraints and variables and these can be added/removed by model.add_cons_vars and model.remove_cons_vars which take care of adding these to model.problem which is the optlang's mathematical model associated with the cobra model.

Reactions are now modeled by two variables, forward and reverse, and these can be seen by accessing reaction.{forward,reverse}_variable and the combined reaction.flux_expression.

Objectives can now easily be made quite advanced by simply crafting the right expression and assigning this as usual to model.objective, see the contraints and objectives notebook.

Temporary changes to a model

Models are large complex objects and copying such objects is inevitably slow. To avoid that, cobrapy has drawn on the experience from the development of cameo to introduce the HistoryManager class and the concept of models as contexts. Now, most changes that can be made to a model such as changing the objective, setting reaction bounds, adding and removing reactions, is reversed upon exit when done inside a context, see the updated getting started notebook.

Improved solution handling

Previously, cobra models lugged around their latest solution to enable providing reaction.{flux,reduced_cost} (formerly reaction.{x,y}). This was problematic because if the model had changed since last optimization, then this would effectively give the wrong result. On top of that, it was not easy to make a change, optimize and get values, and then undo that change to the model without having to copy the whole model object. To solve this, and many similar problem, we have completely refactored cobra.Solution so that model.optimize() now returns a solution and it is the user's responsibility to manage this object. reaction.flux gets its values directly from the model.problem. To sugar the new solution class, fluxes, reduced costs, and shadow prices are now pandas series! Fluxes and reduced costs can be returned as a data frame directlt with the to_frame method.

Sampling

Cobrapy now has flux sampling supported by cobra.flux_analysis.sampling see the sampling notebook.

Loopless models and solutions

Added implementations of CycleFreeFlux and the loopless model of Schellenberger et al.. See the notebook on loopless and simulating

DataFrames as return values

flux_variability_analysis, single_{gene,reaction}_deletion, cobra.flux_analysis.sampling and cobra.util.create_stoichiometric_matrix now return pandas data frames instead of nested dicts as these are more convenient and fun to work with. Pandas (and numpy) are therefore now hard requirements for cobrapy, which should not be a problem for neither linux, windows or mac users as there are reliable wheels for these packages now.

Model medium

model.medium is now a dict and setter for getting boundary feeding reactions and their bounds

Knocking out genes

Addition of cobra.core.Gene.knock_out which can be used to evaluate impact of knocking a gene (and all depending reactions).

Adding boundary reactions

The model class has new method model.add_boundary which can be used to add sink, exchange or demand reactions with the appropriate bounds and prefixes (DM, SK or EX).

Gapfilling

The SMILEY and growMatch implementations were refactored to a single new function cobra.flux_analysis.gapfilling.gapfill which handles both use-cases.

New Output Format in YAML

Models can now be round tripped to/from YAML documents. YAML is a file format that is even more legible than JSON. In the scope of cobrapy, YAML output is intended for diff comparisons between models.

Fixes

  • Handle multiple IDs in Matlab models #345
  • DictList.query behavior changed so that attribute is None if the search parameter is not a regex or string, to enable reactions.query(lambda x: x.boundary)
  • Set charge from notes if not defined elsewhere #352
  • Warnings are no longer issued on package import if soft requirement scipy, python-libsbml is not available.

Deprecated features

These features are now deprecated and slated for complete removal in the next major cobrapy release.

  • The whole cobra.solver module is now deprecated, see New features.
  • ArrayBasedModel / Model.to_array_based_model are deprecated. This formulation makes little sense when handing over the matrix algebra to optlang, for the stoichiometry matrix (aka S), see cobra.util.array.create_stoichiometric_matrix.
  • Metabolite.y in favor of Metabolite.shadow_price
  • Model.add_reaction in favor of Model.add_reactions
  • Reaction.x in favor of Reaction.flux
  • Reaction.y in favor of Reaction.reduced_cost
  • Solution.{x, y, x_dict, y_dict, f} in favor of Solution.{fluxes, reduced_costs}. The setters are also deprecated.
  • phenotype_phase_plane in favor of production_envelope. The plotting capabilities are deprecated, to be re-implemented somewhere else.
  • convert_to_irreverible, revert_to_irreversible, canonical_form deprecated without replacement.
  • check_reaction_bounds deprecated without replacement.
  • optimize_minimal_flux was renamed to pfba

Backwards incompatible changes

  • optknock was completely removed, users are advised to use cameo for this functionality
  • dual_problem was removed
  • cobra.topology was removed, possibly to be reintroduced in a different package
  • fluxvariabilityanalysis results must be transformed to have them work as the previous nested dict, i.e. flux_variability_analysis(model).T should give behavior as previously.
  • In a major linting effort we renamed capitalized modules to lower-case, e.g. cobra.core.Model to cobra.core.model. Imports from cobra are unchanged though.
  • objective coefficients of reactions can now only be set once the reaction is attached to a model.
  • Reaction.{x,y}, Metabolite.y are defunct for legacy solvers.
  • SMILEY and growMatch algorithms are defunct in combination with the legacy solvers.

- Python
Published by hredestig about 9 years ago

cobra -

Release notes for cobrapy 0.6.0

Highlights

In this release we have made major changes to pretty much all corners of cobrapy and we hope that you will enjoy the new features as much as we do, and that any negative impacts on existing workflows will be limited.

The major change is the ongoing move away from cobrapy's internal solver interfaces to those provided by optlang which provides a single unified interface to glpk, cplex and gurobi enhanced by the ability to deal with symbolic expressions. This means formulating complex constraints no longer implies defining the necessary matrix algebra, but instead simply writing the expression and assigning that as an objective to the model.

We feel that this, and the clarified scope and focus attained by separating the topic of linear programming (optlang) and metabolic flux analysis (cobrapy) to two packages is natural and makes both of these tasks less confusing and more fun. We hope that you after trying, feel the same and that in any case you let us know what you think by raising an issue or talking directly to us on gitter or google groups.

New features

The optlang solver interface

The main change is the addition of model.solver which is the optlang interface to the chosen solver (cplex and glpk are currently well supported, gurobi interface is at the time of writing mostly working but improvements are still expected). The solver interface manages variables, constraints and the objective of the model and the task of turning these into a model formulation to be optimized by the solver. From cobrapy's point-of-view, this means that all aspects concerning generating problems, configuring solvers are handed over to optlang and consequently the whole cobra.solver has been deprecated, slated for removal in the next major release of cobrapy.

Importantly, configuring the solver by passing **solver_args or solver='solver' is now instead done by assigning solver to model.solver and then configuring via model.solver.configuration.

Creating new algorithms has been greatly facilitated as it no longer requires formulating objectives and constraints by matrix algebra but instead directly by expressions, e.g. see the implementation of cobra.flux_analysis.moma.add_moma and cobra.flux_analysis.loopless.loopless_solution.

Instead of having only reactions as variables and metabolites as constraints, with optlang, cobrapy now supports arbitrary constraints and variables and these can be added/removed by model.add_cons_vars and model.remove_cons_vars which take care of adding these to model.problem which is the optlang's mathematical model associated with the cobra model.

Reactions are now modeled by two variables, forward and reverse, and these can be seen by accessing reaction.{forward,reverse}_variable and the combined reaction.flux_expression.

Objectives can now easily be made quite advanced by simply crafting the right expression and assigning this as usual to model.objective, see the contraints and objectives notebook.

Temporary changes to a model

Models are large complex objects and copying such objects is inevitably slow. To avoid that, cobrapy has drawn on the experience from the development of cameo to introduce the HistoryManager class and the concept of models as contexts. Now, most changes that can be made to a model such as changing the objective, setting reaction bounds, adding and removing reactions, is reversed upon exit when done inside a context, see the updated getting started notebook.

Improved solution handling

Previously, cobra models lugged around their latest solution to enable providing reaction.{flux,reduced_cost} (formerly reaction.{x,y}). This was problematic because if the model had changed since last optimization, then this would effectively give the wrong result. On top of that, it was not easy to make a change, optimize and get values, and then undo that change to the model without having to copy the whole model object. To solve this, and many similar problem, we have completely refactored cobra.Solution so that model.optimize() now returns a solution and it is the user's responsibility to manage this object. reaction.flux gets its values directly from the model.problem. To sugar the new solution class, fluxes, reduced costs, and shadow prices are now pandas series! Fluxes and reduced costs can be returned as a data frame directly with the to_frame method.

Sampling

Cobrapy now has flux sampling supported by cobra.flux_analysis.sampling see the sampling notebook.

Loopless models and solutions

Added implementations of CycleFreeFlux and the loopless model of Schellenberger et al.. See the notebook on loopless and simulating

DataFrames as return values

flux_variability_analysis, single_{gene,reaction}_deletion, cobra.flux_analysis.sampling and cobra.util.create_stoichiometric_matrix now return pandas data frames instead of nested dicts as these are more convenient and fun to work with. Pandas (and numpy) are therefore now hard requirements for cobrapy, which should not be a problem for neither linux, windows or mac users as there are reliable wheels for these packages now.

Model medium

model.medium is now a dict and setter for getting boundary feeding reactions and their bounds

Knocking out genes

Addition of cobra.core.Gene.knock_out which can be used to evaluate impact of knocking a gene (and all depending reactions).

Adding boundary reactions

The model class has new method model.add_boundary which can be used to add sink, exchange or demand reactions with the appropriate bounds and prefixes (DM, SK or EX).

Fixes

  • Handle multiple IDs in Matlab models #345
  • DictList.query behavior changed so that attribute is None if the search parameter is not a regex or string, to enable reactions.query(lambda x: x.boundary)
  • Set charge from notes if not defined elsewhere #352
  • Warnings are no longer issued on package import if soft requirement scipy, python-libsbml is not available.

Deprecated features

These features are now deprecated and slated for complete removal in the next major cobrapy release.

  • The whole cobra.solver module is now deprecated, see New features.
  • ArrayBasedModel / Model.to_array_based_model are deprecated. This formulation makes little sense when handing over the matrix algebra to optlang, for the stoichiometry matrix (aka S), see cobra.util.array.create_stoichiometric_matrix.
  • Metabolite.y in favor of Metabolite.shadow_price
  • Model.add_reaction in favor of Model.add_reactions
  • Reaction.x in favor of Reaction.flux
  • Reaction.y in favor of Reaction.reduced_cost
  • Solution.{x, y, x_dict, y_dict, f} in favor of Solution.{fluxes, reduced_costs}. The setters are also deprecated.
  • phenotype_phase_plane in favor of production_envelope. The plotting capabilities are deprecated, to be re-implemented somewhere else.
  • convert_to_irreverible, revert_to_irreversible, canonical_form deprecated without replacement.
  • check_reaction_bounds deprecated without replacement.
  • optimize_minimal_flux was renamed to pfba

Backwards incompatible changes

  • optknock was completely removed, users are advised to use cameo for this functionality
  • dual_problem was removed
  • gapfilling algorithms were removed without replacement, to be re-introduced in a different package
  • cobra.topology was removed, possibly to be reintroduced in a different package
  • fluxvariabilityanalysis results must be transformed to have them work as the previous nested dict, i.e. flux_variability_analysis(model).T should give behavior as previously.
  • In a major linting effort we renamed capitalized modules to lower-case, e.g. cobra.core.Model to cobra.core.model. Imports from cobra are unchanged though.
  • objective coefficients of reactions can now only be set once the reaction is attached to a model.
  • Reaction.{x,y}, Metabolite.y are defunct for legacy solvers.

- Python
Published by hredestig about 9 years ago

cobra - 0.6.0a6

Release notes for cobrapy 0.6.0

Highlights

In this release we have made major changes to pretty much all corners of cobrapy and we hope that you will enjoy the new features as much as we do, and that any negative impacts on existing workflows will be limited.

The major change is the ongoing move away from cobrapy's internal solver interfaces to those provided by optlang which provides a single unified interface to glpk, cplex and gurobi enhanced by the ability to deal with symbolic expressions. This means formulating complex constraints no longer implies defining the necessary matrix algebra, but instead simply writing the expression and assigning that as an objective to the model.

We feel that this, and the clarified scope and focus attained by separating the topic of linear programming (optlang) and metabolic flux analysis (cobrapy) to two packages is natural and makes both of these tasks less confusing and more fun. We hope that you after trying, feel the same and that in any case you let us know what you think by raising an issue or talking directly to us on gitter or google groups.

New features

The optlang solver interface

The main change is the addition of model.solver which is the optlang interface to the chosen solver (cplex and glpk are currently well supported, gurobi interface is at the time of writing mostly working but improvements are still expected). The solver interface manages variables, constraints and the objective of the model and the task of turning these into a model formulation to be optimized by the solver. From cobrapy's point-of-view, this means that all aspects concerning generating problems, configuring solvers are handed over to optlang and consequently the whole cobra.solver has been deprecated, slated for removal in the next major release of cobrapy.

Importantly, configuring the solver by passing **solver_args or solver='solver' is now instead done by assigning solver to model.solver and then configuring via model.solver.configuration.

Creating new algorithms has been greatly facilitated as it no longer requires formulating objectives and constraints by matrix algebra but instead directly by expressions, e.g. see the implementation of cobra.flux_analysis.moma.add_moma and cobra.flux_analysis.loopless.loopless_solution.

Instead of having only reactions as variables and metabolites as constraints, with optlang, cobrapy now supports arbitrary constraints and variables and these can be added/removed by model.add_cons_vars and model.remove_cons_vars which take care of adding these to model.problem which is the optlang's mathematical model associated with the cobra model.

Reactions are now modeled by two variables, forward and reverse, and these can be seen by accessing reaction.{forward,reverse}_variable and the combined reaction.flux_expression.

Objectives can now easily be made quite advanced by simply crafting the right expression and assigning this as usual to model.objective, see the contraints and objectives notebook.

Temporary changes to a model

Models are large complex objects and copying such objects is inevitably slow. To avoid that, cobrapy has drawn on the experience from the development of cameo to introduce the HistoryManager class and the concept of models as contexts. Now, most changes that can be made to a model such as changing the objective, setting reaction bounds, adding and removing reactions, is reversed upon exit when done inside a context, see the updated getting started notebook.

Improved solution handling

Previously, cobra models lugged around their latest solution to enable providing reaction.{flux,reduced_cost} (formerly reaction.{x,y}). This was problematic because if the model had changed since last optimization, then this would effectively give the wrong result. On top of that, it was not easy to make a change, optimize and get values, and then undo that change to the model without having to copy the whole model object. To solve this, and many similar problem, we have completely refactored cobra.Solution so that model.optimize() now returns a solution and it is the user's responsibility to manage this object. reaction.flux gets its values directly from the model.problem. To sugar the new solution class, fluxes, reduced costs, and shadow prices are now pandas series!

Sampling

Cobrapy now has flux sampling supported by cobra.flux_analysis.sampling see the sampling notebook.

Loopless models and solutions

Added implementations of CycleFreeFlux and the loopless model of Schellenberger et al.. See the notebook on loopless and simulating

DataFrames as return values

flux_variability_analysis, single_{gene,reaction}_deletion, cobra.flux_analysis.sampling and cobra.util.create_stoichiometric_matrix now return pandas data frames instead of nested dicts as these are more convenient and fun to work with. Pandas (and numpy) are therefore now hard requirements for cobrapy, which should not be a problem for neither linux, windows or mac users as there are reliable wheels for these packages now.

Model medium

model.medium is now a dict and setter for getting boundary feeding reactions and their bounds

Knocking out genes

Addition of cobra.core.Gene.knock_out which can be used to evaluate impact of knocking a gene (and all depending reactions).

Adding boundary reactions

The model class has new method model.add_boundary which can be used to add sink, exchange or demand reactions with the appropriate bounds and prefixes (DM, SK or EX).

Fixes

  • Handle multiple IDs in Matlab models #345
  • DictList.query behavior changed so that attribute is None if the search parameter is not a regex or string, to enable reactions.query(lambda x: x.boundary)
  • Set charge from notes if not defined elsewhere #352
  • Warnings are no longer issued on package import if soft requirement scipy, python-libsbml is not available.

Deprecated features

These features are now deprecated and slated for complete removal in the next major cobrapy release.

  • The whole cobra.solver module is now deprecated, see New features.
  • ArrayBasedModel / Model.to_array_based_model are deprecated. This formulation makes little sense when handing over the matrix algebra to optlang, for the stoichiometry matrix (aka S), see cobra.util.array.create_stoichiometric_matrix.
  • Metabolite.y in favor of Metabolite.shadow_price
  • Model.add_reaction in favor of Model.add_reactions
  • Reaction.x in favor of Reaction.flux
  • Reaction.y in favor of Reaction.reduced_cost
  • Solution.{x, y, x_dict, y_dict, f} in favor of Solution.{fluxes, reduced_costs}. The setters are also deprecated.
  • phenotype_phase_plane in favor of production_envelope. The plotting capabilities are deprecated, to be re-implemented somewhere else.
  • convert_to_irreverible, revert_to_irreversible, canonical_form deprecated without replacement.
  • check_reaction_bounds deprecated without replacement.
  • optimize_minimal_flux was renamed to pfba

Backwards incompatible changes

  • optknock was completely removed, users are advised to use cameo for this functionality
  • dual_problem was removed
  • gapfilling algorithms were removed without replacement, to be re-introduced in a different package
  • cobra.topology was removed, possibly to be reintroduced in a different package
  • fluxvariabilityanalysis results must be transformed to have them work as the previous nested dict, i.e. flux_variability_analysis(model).T should give behavior as previously.
  • In a major linting effort we renamed capitalized modules to lower-case, e.g. cobra.core.Model to cobra.core.model. Imports from cobra are unchanged though.
  • objective coefficients of reactions can now only be set once the reaction is attached to a model.
  • Reaction.{x,y}, Metabolite.y are defunct for legacy solvers.

- Python
Published by hredestig about 9 years ago

cobra - 0.6.0a4

Release notes for cobrapy 0.6.0

Highlights

In this release we have made major changes to pretty much all corners of cobrapy and we hope that you will enjoy the new features as much as we do, and that any negative impacts on existing workflows will be limited.

The major change is the ongoing move away from cobrapy's internal solver interfaces to those provided by optlang which provides a single unified interface to glpk, cplex and gurobi enhanced by the ability to deal with symbolic expressions. This means formulating complex constraints no longer implies defining the necessary matrix algebra, but instead simply writing the expression and assigning that as an objective to the model.

We feel that this, and the clarified scope and focus attained by separating the topic of linear programming (optlang) and metabolic flux analysis (cobrapy) to two packages is natural and makes both of these tasks less confusing and more fun. We hope that you after trying, feel the same and that in any case you let us know what you think by raising an issue or talking directly to us on gitter or google groups.

New features

The optlang solver interface

The main change is the addition of model.solver which is the optlang interface to the chosen solver (cplex and glpk are currently well supported, gurobi interface is at the time of writing mostly working but improvements are still expected). The solver interface manages variables, constraints and the objective of the model and the task of turning these into a model formulation to be optimized by the solver. From cobrapy's point-of-view, this means that all aspects concerning generating problems, configuring solvers are handed over to optlang and consequently the whole cobra.solver has been deprecated, slated for removal in the next major release of cobrapy.

Importantly, configuring the solver by passing **solver_args or solver='solver' is now instead done by assigning solver to model.solver and then configuring via model.solver.configuration.

Creating new algorithms has been greatly facilitated as it no longer requires formulating objectives and constraints by matrix algebra but instead directly by expressions, e.g. see the implementation of cobra.flux_analysis.moma.add_moma and cobra.flux_analysis.loopless.loopless_solution.

Instead of having only reactions as variables and metabolites as constraints, with optlang, cobrapy now supports arbitrary constraints and variables and these can be added/removed by model.add_cons_vars and model.remove_cons_vars which take care of adding these to model.problem which is the optlang's mathematical model associated with the cobra model.

Reactions are now modeled by two variables, forward and reverse, and these can be seen by accessing reaction.{forward,reverse}_variable and the combined reaction.flux_expression.

Objectives can now easily be made quite advanced by simply crafting the right expression and assigning this as usual to model.objective, see the contraints and objectives notebook.

Temporary changes to a model

Models are large complex objects and copying such objects is inevitably slow. To avoid that, cobrapy has drawn on the experience from the development of cameo to introduce the HistoryManager class and the concept of models as contexts. Now, most changes that can be made to a model such as changing the objective, setting reaction bounds, adding and removing reactions, is reversed upon exit when done inside a context, see the updated getting started notebook.

Improved solution handling

Previously, cobra models lugged around their latest solution to enable providing reaction.{flux,reduced_cost} (formerly reaction.{x,y}). This was problematic because if the model had changed since last optimization, then this would effectively give the wrong result. On top of that, it was not easy to make a change, optimize and get values, and then undo that change to the model without having to copy the whole model object. To solve this, and many similar problem, we have completely refactored cobra.Solution so that model.optimize() now returns a solution and it is the user's responsibility to manage this object. reaction.flux gets its values directly from the model.problem. To sugar the new solution class, fluxes, reduced costs, and shadow prices are now pandas series!

Sampling

Cobrapy now has flux sampling supported by cobra.flux_analysis.sampling see the sampling notebook.

Loopless models and solutions

Added implementations of CycleFreeFlux and the loopless model of Schellenberger et al.. See the notebook on loopless and simulating

DataFrames as return values

flux_variability_analysis, single_{gene,reaction}_deletion, cobra.flux_analysis.sampling and cobra.util.create_stoichiometric_matrix now return pandas data frames instead of nested dicts as these are more convenient and fun to work with. Pandas (and numpy) are therefore now hard requirements for cobrapy, which should not be a problem for neither linux, windows or mac users as there are reliable wheels for these packages now.

Model medium

model.medium is now a dict and setter for getting boundary feeding reactions and their bounds

Fixes

  • Handle multiple IDs in Matlab models #345
  • DictList.query behavior changed so that attribute is None if the search parameter is not a regex or string, to enable reactions.query(lambda x: x.boundary)
  • Set charge from notes if not defined elsewhere #352
  • Warnings are no longer issued on package import if soft requirement scipy, python-libsbml is not available.

Deprecated features

These features are now deprecated and slated for complete removal in the next major cobrapy release.

  • The whole cobra.solver module is now deprecated, see New features.
  • ArrayBasedModel / Model.to_array_based_model are deprecated. This formulation makes little sense when handing over the matrix algebra to optlang, for the stoichiometry matrix (aka S), see cobra.util.array.create_stoichiometric_matrix.
  • Metabolite.y in favor of Metabolite.shadow_price
  • Model.add_reaction in favor of Model.add_reactions
  • Reaction.x in favor of Reaction.flux
  • Reaction.y in favor of Reaction.reduced_cost
  • Solution.{x, y, x_dict, y_dict, f} in favor of Solution.{fluxes, reduced_costs}. The setters are also deprecated.
  • phenotype_phase_plane in favor of production_envelope. The plotting capabilities are deprecated, to be re-implemented somewhere else.
  • convert_to_irreverible, revert_to_irreversible, canonical_form deprecated without replacement.
  • check_reaction_bounds deprecated without replacement.
  • optimize_minimal_flux was renamed to pfba

Backwards incompatible changes

  • optknock was completely removed, users are advised to use cameo for this functionality
  • dual_problem was removed
  • gapfilling algorithms were removed without replacement, to be re-introduced in a different package
  • cobra.topology was removed, possibly to be reintroduced in a different package
  • fluxvariabilityanalysis results must be transformed to have them work as the previous nested dict, i.e. flux_variability_analysis(model).T should give behavior as previously.
  • In a major linting effort we renamed capitalized modules to lower-case, e.g. cobra.core.Model to cobra.core.model. Imports from cobra are unchanged though.
  • objective coefficients of reactions can now only be set once the reaction is attached to a model.
  • Reaction.{x,y}, Metabolite.y are defunct for legacy solvers.

- Python
Published by hredestig about 9 years ago

cobra - 0.5.11

See documentation for features.

- Python
Published by hredestig about 9 years ago

cobra - 0.6.0a2

Release notes for cobrapy 0.6.0

Highlights

In this release we have made major changes to pretty much all corners of cobrapy and we hope that you will enjoy the new features as much as we do, and that any negative impacts on existing workflows will be limited.

The major change is the ongoing move away from cobrapy's internal solver interfaces to those provided by optlang which provides a single unified interface to glpk, cplex and gurobi enhanced by the ability to deal with symbolic expressions. This means formulating complex constraints no longer implies defining the necessary matrix algebra, but instead simply writing the expression and assigning that as an objective to the model.

We feel that this, and the clarified scope and focus attained by separating the topic of linear programming (optlang) and metabolic flux analysis (cobrapy) to two packages is natural and makes both of these tasks less confusing and more fun. We hope that you after trying, feel the same and that in any case you let us know what you think by raising an issue or talking directly to us on gitter or google groups.

New features

The optlang solver interface

The main change is the addition of model.solver which is the optlang interface to the chosen solver (cplex and glpk are currently well supported, gurobi interface is at the time of writing mostly working but improvements are still expected). The solver interface manages variables, constraints and the objective of the model and the task of turning these into a model formulation to be optimized by the solver. From cobrapy's point-of-view, this means that all aspects concerning generating problems, configuring solvers are handed over to optlang and consequently the whole cobra.solver has been deprecated, slated for removal in the next major release of cobrapy.

Importantly, configuring the solver by passing **solver_args or solver='solver' is now instead done by assigning solver to model.solver and then configuring via model.solver.configuration.

Creating new algorithms has been greatly facilitated as it no longer requires formulating objectives and constraints by matrix algebra but instead directly by expressions, e.g. see the implementation of cobra.flux_analysis.moma.add_moma and cobra.flux_analysis.loopless.loopless_solution.

Instead of having only reactions as variables and metabolites as constraints, with optlang, cobrapy now supports arbitrary constraints and variables and these can be added/removed by model.add_cons_vars and model.remove_cons_vars which take care of adding these to model.problem which is the optlang's mathematical model associated with the cobra model.

Reactions are now modeled by two variables, forward and reverse, and these can be seen by accessing reaction.{forward,reverse}_variable and the combined reaction.flux_expression.

Objectives can now easily be made quite advanced by simply crafting the right expression and assigning this as usual to model.objective, see the contraints and objectives notebook.

Temporary changes to a model

Models are large complex objects and copying such objects is inevitably slow. To avoid that, cobrapy has drawn on the experience from the development of cameo to introduce the HistoryManager class and the concept of models as contexts. Now, most changes that can be made to a model such as changing the objective, setting reaction bounds, adding and removing reactions, is reversed upon exit when done inside a context, see the updated getting started notebook.

Improved solution handling

Previously, cobra models lugged around their latest solution to enable providing reaction.{flux,reduced_cost} (formerly reaction.{x,y}). This was problematic because if the model had changed since last optimization, then this would effectively give the wrong result. On top of that, it was not easy to make a change, optimize and get values, and then undo that change to the model without having to copy the whole model object. To solve this, and many similar problem, we have completely refactored cobra.Solution so that model.optimize() now returns a solution and it is the user's responsibility to manage this object. reaction.flux gets its values directly from the model.problem. To sugar the new solution class, fluxes, reduced costs, and shadow prices are now pandas series!

Sampling

Cobrapy now has flux sampling supported by cobra.flux_analysis.sampling see the sampling notebook.

Loopless models and solutions

Added implementations of CycleFreeFlux and the loopless model of Schellenberger et al.. See the notebook on loopless and simulating

DataFrames as return values

flux_variability_analysis, single_{gene,reaction}_deletion, cobra.flux_analysis.sampling and cobra.util.create_stoichiometric_matrix now return pandas data frames instead of nested dicts as these are more convenient and fun to work with. Pandas (and numpy) are therefore now hard requirements for cobrapy, which should not be a problem for neither linux, windows or mac users as there are reliable wheels for these packages now.

Model medium

model.medium is now a dict and setter for getting boundary feeding reactions and their bounds

Fixes

  • Handle multiple IDs in Matlab models #345
  • DictList.query behavior changed so that attribute is None if the search parameter is not a regex or string, to enable reactions.query(lambda x: x.boundary)
  • Set charge from notes if not defined elsewhere #352
  • Warnings are no longer issued on package import if soft requirement scipy, python-libsbml is not available.

Deprecated features

These features are now deprecated and slated for complete removal in the next major cobrapy release.

  • The whole cobra.solver module is now deprecated, see New features.
  • ArrayBasedModel / Model.to_array_based_model are deprecated. This formulation makes little sense when handing over the matrix algebra to optlang, for the stoichiometry matrix (aka S), see cobra.util.array.create_stoichiometric_matrix.
  • Metabolite.y in favor of Metabolite.shadow_price
  • Model.add_reaction in favor of Model.add_reactions
  • Reaction.x in favor of Reaction.flux
  • Reaction.y in favor of Reaction.reduced_cost
  • Solution.{x, y, x_dict, y_dict, f} in favor of Solution.{fluxes, reduced_costs}. The setters are also deprecated.
  • phenotype_phase_plane in favor of production_envelope. The plotting capabilities are deprecated, to be re-implemented somewhere else.
  • convert_to_irreverible, revert_to_irreversible, canonical_form deprecated without replacement.
  • check_reaction_bounds deprecated without replacement.

Backwards incompatible changes

  • optknock was completely removed, users are advised to use cameo for this functionality
  • dual_problem was removed
  • gapfilling algorithms were removed without replacement, to be re-introduced in a different package
  • cobra.topology was removed, possibly to be reintroduced in a different package
  • fluxvariabilityanalysis results must be transformed to have them work as the previous nested dict, i.e. flux_variability_analysis(model).T should give behavior as previously.
  • In a major linting effort we renamed capitalized modules to lower-case, e.g. cobra.core.Model to cobra.core.model. Imports from cobra are unchanged though.
  • objective coefficients of reactions can now only be set once the reaction is attached to a model.
  • Reaction.{x,y}, Metabolite.y are defunct for legacy solvers.

- Python
Published by hredestig about 9 years ago

cobra - 0.6.0a1

Release notes for cobrapy 0.6.0

Highlights

In this release we have made major changes to pretty much all corners of cobrapy but we hope that any negative impact on existing workflows will still be limited. The major change is the ongoing move away from cobrapy's internal solver interfaces to those provided by optlang which provides a single unified interface to glpk, cplex and gurobi enhanced by the ability to deal with symbolic expressions. This means formulating complex constraints no longer implies defining the necessary matrix algebra, but instead simply writing the expression and assigning that as on objective to the model.

We feel that the this, and the clarified scope and focus attained by separating the topic of linear programming (optlang) and metabolic flux analysis (cobrapy) to two packages is natural and makes both of these tasks less confusing and more fun. We hope that you after trying, feel the same and that in any case you let us know what you think by raising an issue or talking directly to us on gitter or google groups.

New features

The optlang solver interface

The main change is the addition of model.solver which is the optlang interface to the chosen solver (cplex and glpk are currently well supported, gurobi interface is at the time of writing mostly working but improvements are still expected). The solver interface manages variables, constraints and the objective of the model and the task of turning these into a model formulation to be optimized by the solver. From cobrapy's point-of-view, this means that all aspects concerning generating problems, configuring solvers are handed over to optlang and consequently the whole cobra.solver has been deprecated, slated for removal in the next major release of cobrapy.

Importantly, configuring the solver by passing **solver_args or solver='solver' is now instead done by assigning solver to model.solver and then configuring via model.solver.configuration.

Creating new algorithms has been greatly facilitated as it no longer requires formulating objectives and constraints by matrix algebra but instead directly by expressions, e.g. see the implementation of cobra.flux_analysis.moma.add_moma and cobra.flux_analysis.loopless.loopless_solution.

Instead of having only reactions as variables and metabolites as constraints, with optlang, cobrapy now supports arbitrary constraints and variables and these can be added/removed by model.add_cons_vars and model.remove_cons_vars which take care of adding these to model.problem which is the optlang's mathematical model associated with the cobra model.

Reactions are now modeled by two variables, forward and reverse, and these can be seen by accessing reaction.{forward,reverse}_variable and the combined reaction.flux_expression.

Objectives can now easily be made quite advanced by simply crafting the right expression and assigning this as usual to model.objective, see the contraints and objectives notebook.

Temporary changes to a model

Models are large complex objects and copying such objects is inevitably slow. To avoid that, cobrapy has drawn on the experience from the development of cameo to introduce the HistoryManager class and the concept of models as contexts. Now, most changes that can be made to a model such as changing the objective, setting reaction bounds, adding and removing reactions, is reversed upon exit when done inside a context, see the updated getting started notebook.

Improved solution handling

Previously, cobra models lugged around their latest solution to enable providing reaction.{flux,reduced_cost} (formerly reaction.{x,y}). This was problematic because if the model had changed since last optimization, then this would effectively give the wrong result. On top of that, it was not easy to make a change, optimize and get values, and then undo that change to the model without having to copy the whole model object. To solve this, and many similar problem, we have completely refactored cobra.Solution so that model.optimize() now returns a solution and it is the user's responsibility to manage this object. reaction.flux gets its values directly from the model.problem. To sugar the new solution class, fluxes, reduced costs, and shadow prices are now pandas series!

Sampling

Cobrapy now has flux sampling supported by cobra.flux_analysis.sampling see the sampling notebook.

Loopless models and solutions

Added implementations of CycleFreeFlux and the loopless model of Schellenberger et al.. See the notebook on loopless and simulating

DataFrames as return values

flux_variability_analysis, single_{gene,rection}_deletion, cobra.flux_analysis.sampling and cobra.util.create_stoichiometric_array now return a pandas data frame instead of nested dicts as these are more convenient and fun to work with. Pandas (and numpy) are therefore now hard requirements for cobrapy, which should not be a problem for neither linux, windows or mac users as there are reliable wheels for these packages now.

Model medium

model.medium is now a dict and setter for getting boundary feeding reactions and their bounds

Fixes

  • Handle multiple IDs in Matlab models #345
  • DictList.query behavior changed so that attribute is None if the search parameter is not a regex or string, to enable reactions.query(lambda x: x.boundary)
  • Set charge from notes if not defined elsewhere #352
  • Warnings are no longer issued on package import if soft requirement scipy, python-libsbml is not available.

Deprecated features

These features are now deprecated and slated for complete removal in the next major cobrapy release.

  • The whole cobra.solver module is now deprecated, see New features.
  • ArrayBasedModel / Model.to_array_based_model are deprecated. This formulation makes little sense when handing over the matrix algebra to optlang, for the stoichiometry matrix (aka S), see cobra.util.array.create_stoichiometric_array.
  • Metabolite.y in favor of Metabolite.shadow_price
  • Model.add_reaction in favor of Model.add_reactions
  • Reaction.x in favor of Reaction.flux
  • Reaction.y in favor of Reaction.reduced_cost
  • Solution.{x, y, x_dict, y_dict, f} in favor of Solution.{fluxes, reduced_costs}. The setters are also deprecated.
  • phenotype_phase_plane in favor of production_envelope. The plotting capabilities are deprecated, to be re-implemented somewhere else.
  • convert_to_irreverible, revert_to_irreversible, canonical_form deprecated without replacement.
  • check_reaction_bounds deprecated without replacement.

Backwards incompatible changes

  • optknock was completely removed, users are advised to use cameo for this functionality
  • dual_problem was removed
  • gapfilling algorithms were removed without replacement, to be re-introduced in a different package
  • cobra.topology was removed, possibly to be reintroduced in a different package
  • fluxvariabilityanalysis results must be transformed to have them work as the previous nested dict, i.e. flux_variability_analysis(model).T should give behavior as previously.
  • In a major linting effort we renamed capitalized modules to lower-case, e.g. cobra.core.Model to cobra.core.model. Imports from cobra are unchanged though.
  • objective coefficients of reactions can now only be set once the reaction is attached to a model.
  • Reaction.{x,y}, Metabolite.y are defunct for legacy solvers.

- Python
Published by hredestig about 9 years ago

cobra - 0.4.0b2

Further updates to I/O system and miscellaneous bugfixes.

- Python
Published by aebrahim almost 11 years ago

cobra - 0.4.0b1

The 0.4.0b1 release includes many new features over 0.3.2, most notably native support for SBML3 with fbc version 2. It is also now dual-licensed under both GPL and LGPL v2.

- Python
Published by aebrahim almost 11 years ago

cobra -

- Python
Published by aebrahim almost 11 years ago

cobra -

- Python
Published by aebrahim almost 11 years ago

cobra -

- Python
Published by aebrahim almost 11 years ago

cobra - 0.3.2

This is a minor bugfix release.

It fixes bugs in edge cases with savemat, cglpk, and cplex.

- Python
Published by aebrahim about 11 years ago

cobra - 0.3.1

This is a minor bugfix release.

In addition to minor bugfixes, it brings support for OS 10.10 Yosemite, simplifies installation and adds reaction construction from strings.

- Python
Published by aebrahim over 11 years ago

cobra - 0.3.0

This is a major release from 0.2.1, with many new features added. A brief summary is below: - Revamped faster and simpler solver interface - New "cglpk" solver to replace "pyglpk" as the default solver (compatible with the latest version of GLPK) - Support for "exact" solving (#126, 41d91e8b2bf9c7b6c58b5315a07768c3c460b2af) - Rewritten documentation now available as IPython notebooks - Major performance improvements to deletions and FVA - More flux analysis tools (pFBA and phenotypic phase planes, loopless FBA) - SBML fbc support - Python 3 support - Improvements to ArrayBasedModel - Read-only attributes for gene/reaction/metabolite relationships

- Python
Published by aebrahim over 11 years ago

cobra - 0.3.0b4

The following features were added: - Improvements to solver interface - Support for exact solving with esolver (Qsopt_ex) (#126) - Support for Mosek (f79248f89673025e37f1b9aa796bd8cb28ba157f) - Support for "exact" solving with glpk (through cglpk) (41d91e8b2bf9c7b6c58b5315a07768c3c460b2af) - cglpk is now the preferred binding to glpk (#129) - Implementation of loopless FBA (#133) - Update documentation to IPython notebooks (0e380963d3428d0fbd40135032efd24810048ce4)

- Python
Published by aebrahim over 11 years ago

cobra -

Improvements over 0.3.0b1:
- installation improvements - updates to documentation - misc bugfixes in - qp - cglpk solver - double deletion multiprocessing

- Python
Published by aebrahim almost 12 years ago

cobra -

Changes in 0.3.0b1: - faster solver interface - faster fva and single/double deletions with new interface - cython-based glpk solver - more flux analysis tools (pFBA and phenotypic phase planes) - sbml fbc support - improvements to ArrayBasedModel - access read-only attributes for gene/reaction/metabolite relationships - simplified installation - python3 support

- Python
Published by aebrahim almost 12 years ago

cobra -

- Python
Published by aebrahim almost 13 years ago

cobra -

- Python
Published by aebrahim almost 13 years ago